M Madan Babu

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. ncbi request reprint Evolutionary dynamics of prokaryotic transcriptional regulatory networks
    M Madan Babu
    National Center for Biotechnology Information, National Institutes of Health, MD 20894, USA
    J Mol Biol 358:614-33. 2006
  2. ncbi request reprint Computational approaches to study transcriptional regulation
    M Madan Babu
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Biochem Soc Trans 36:758-65. 2008
  3. pmc Epithelial organisation revealed by a network of cellular contacts
    Luis M Escudero
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nat Commun 2:526. 2011
  4. pmc Cellular strategies for regulating functional and nonfunctional protein aggregation
    Jörg Gsponer
    Centre for High Throughput Biology, Department of Biochemistry and Molecular Biology, University of British Columbia, East Mall, Vancouver V6T 1Z4, Canada
    Cell Rep 2:1425-37. 2012
  5. pmc Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions
    Roland A Pache
    Structural and Computational Biology, Institute for Research in Biomedicine Barcelona, c Baldiri Reixac 10 12, 08028 Barcelona, Spain
    BMC Syst Biol 3:74. 2009
  6. doi request reprint Intrinsically disordered proteins: regulation and disease
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom
    Curr Opin Struct Biol 21:432-40. 2011
  7. doi request reprint Early Career Research Award Lecture. Structure, evolution and dynamics of transcriptional regulatory networks
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Biochem Soc Trans 38:1155-78. 2010
  8. ncbi request reprint General trends in the evolution of prokaryotic transcriptional regulatory networks
    M Madan Babu
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Dyn 3:66-80. 2007
  9. pmc A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Bacteriol 188:2761-73. 2006
  10. ncbi request reprint Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 5:2354-63. 2006

Detail Information

Publications66

  1. ncbi request reprint Evolutionary dynamics of prokaryotic transcriptional regulatory networks
    M Madan Babu
    National Center for Biotechnology Information, National Institutes of Health, MD 20894, USA
    J Mol Biol 358:614-33. 2006
    ..The methods for biological network analysis introduced here can be applied generally to study other networks, and these predictions can be used to guide specific experiments...
  2. ncbi request reprint Computational approaches to study transcriptional regulation
    M Madan Babu
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Biochem Soc Trans 36:758-65. 2008
    ....
  3. pmc Epithelial organisation revealed by a network of cellular contacts
    Luis M Escudero
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nat Commun 2:526. 2011
    ..The approach permits characterization, quantification and classification of normal and perturbed epithelia, and establishes a framework for understanding molecular mechanisms that underpin the architecture of complex tissues...
  4. pmc Cellular strategies for regulating functional and nonfunctional protein aggregation
    Jörg Gsponer
    Centre for High Throughput Biology, Department of Biochemistry and Molecular Biology, University of British Columbia, East Mall, Vancouver V6T 1Z4, Canada
    Cell Rep 2:1425-37. 2012
    ..This strategy may prevent formation of undesirable aggregates and keep functional assemblies/aggregates under control...
  5. pmc Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions
    Roland A Pache
    Structural and Computational Biology, Institute for Research in Biomedicine Barcelona, c Baldiri Reixac 10 12, 08028 Barcelona, Spain
    BMC Syst Biol 3:74. 2009
    ....
  6. doi request reprint Intrinsically disordered proteins: regulation and disease
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom
    Curr Opin Struct Biol 21:432-40. 2011
    ..e., molecular titration), thereby causing an imbalance in signaling pathways. We discuss the regulation of IDPs, address implications for signaling, disease and drug development, and outline directions for future research...
  7. doi request reprint Early Career Research Award Lecture. Structure, evolution and dynamics of transcriptional regulatory networks
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Biochem Soc Trans 38:1155-78. 2010
    ..Finally, I conclude by discussing open questions for future research and highlighting the implications for evolution, development, disease and applications such as genetic engineering...
  8. ncbi request reprint General trends in the evolution of prokaryotic transcriptional regulatory networks
    M Madan Babu
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Dyn 3:66-80. 2007
    ..In turn, as phylogenetic diversification proceeds, this process appears to have favored repeated convergence to scale-free-like structures, albeit with different regulatory hubs...
  9. pmc A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Bacteriol 188:2761-73. 2006
    ..The website, along with additional information on the biosynthetic pathway, statistics on predicted lipoproteins, and related figures, is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop/...
  10. ncbi request reprint Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 5:2354-63. 2006
    ..Based on these observations, we also propose that genome-wide chromatin immunoprecipitation data might be useful to systematically uncover long-range chromatin looping effects in gene expression...
  11. pmc The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:6505-20. 2006
    ..We also use the WRKY-GCM1 superfamily as an example to illustrate the importance of transposons in the emergence of new TFs in different lineages...
  12. ncbi request reprint Eukaryotic gene regulation in three dimensions and its impact on genome evolution
    M Madan Babu
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Curr Opin Genet Dev 18:571-82. 2008
    ..We then address implications for human diseases and outline new directions for future research...
  13. ncbi request reprint Structure and evolution of transcriptional regulatory networks
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Curr Opin Struct Biol 14:283-91. 2004
    ..Interactions are conserved to varying degrees among genomes. Insights from the structure and evolution of these networks can be translated into predictions and used for engineering of the regulatory networks of different organisms...
  14. ncbi request reprint Functional determinants of transcription factors in Escherichia coli: protein families and binding sites
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, UK
    Trends Genet 19:75-9. 2003
    ....
  15. ncbi request reprint Did the loss of sigma factors initiate pseudogene accumulation in M. leprae?
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Trends Microbiol 11:59-61. 2003
    ....
  16. pmc Evolution of transcription factors and the gene regulatory network in Escherichia coli
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 31:1234-44. 2003
    ....
  17. pmc NCI: A server to identify non-canonical interactions in protein structures
    M Madan Babu
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 31:3345-8. 2003
    ..In addition, the user can view the RasMol image highlighting the interactions in the protein structure and download the RasMol script. The NCI server is available at: http://www.mrc-lmb.cam.ac.uk/genomes/nci/...
  18. ncbi request reprint DOLOP--database of bacterial lipoproteins
    M Madan Babu
    Centre for Biotechnology, Anna University, Chennai 600025, India
    Bioinformatics 18:641-3. 2002
    ..Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility...
  19. ncbi request reprint Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda 20894, USA
    J Mol Biol 360:213-27. 2006
    ..We believe that the results presented here might provide a framework for testing the role of co-regulatory associations in eukaryotic transcriptional control...
  20. ncbi request reprint Gene regulatory network growth by duplication
    Sarah A Teichmann
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nat Genet 36:492-6. 2004
    ..In addition, we conclude that evolution has been incremental, rather than making entire regulatory circuits or motifs by duplication with inheritance of interactions...
  21. ncbi request reprint Solitary and repetitive binding motifs for the AP2 complex alpha-appendage in amphiphysin and other accessory proteins
    Lene E Olesen
    Laboratory of Molecular Biology, Medical Research Council, Neurobiology Division, Hills Road, Cambridge CB2 2QH, United Kingdom
    J Biol Chem 283:5099-109. 2008
    ..We describe the optimal sequence of the FXDXF motif using thermodynamic and structural data and show how sequence variation controls the affinities of these motifs for the alpha-appendage...
  22. ncbi request reprint Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 360:204-12. 2006
    ..Thus, an "over-engineered" backup system in the form of distributed architecture is likely to be a major determinant of the "evolvability" of the gene expression in organisms faced with environmental diversity...
  23. pmc Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:3994-4006. 2005
    ....
  24. pmc Tight regulation of unstructured proteins: from transcript synthesis to protein degradation
    Jörg Gsponer
    Medical Research Council MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Science 322:1365-8. 2008
    ..Fidelity in signaling may require that most IUPs be available in appropriate amounts and not present longer than needed...
  25. ncbi request reprint Statistical analysis of domains in interacting protein pairs
    Tom M W Nye
    Medical Research Council Biostatistics Unit, Cambridge, UK
    Bioinformatics 21:993-1001. 2005
    ..Our approach is driven by the need to assess the evidence for physical contacts between domains in a statistically rigorous way...
  26. ncbi request reprint Conservation of gene co-regulation in prokaryotes and eukaryotes
    Sarah A Teichmann
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Trends Biotechnol 20:407-10; discussion 410. 2002
    ..Our analysis reveals that the number of conserved co-regulated genes is small in eukaryotes, as has been shown previously in prokaryotes, indicating that there are extensive variations in the gene regulatory network across organisms...
  27. pmc Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 372:1108-22. 2007
    ....
  28. ncbi request reprint Methods to reconstruct and compare transcriptional regulatory networks
    M Madan Babu
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Methods Mol Biol 541:163-80. 2009
    ..In this chapter, we will focus in detail on the first approach and describe methods to reconstruct and analyze the transcriptional regulatory networks of uncharacterized organisms by using a known regulatory network as a template...
  29. ncbi request reprint Transcript stability in the protein interaction network of Escherichia coli
    Sarath Chandra Janga
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK CB2 0QH
    Mol Biosyst 5:154-62. 2009
    ..Our results provide a direct link between mRNA stability and centrality of a protein in PPI network indicating the importance of post-transcriptional mechanisms on nascent RNAs in the cell...
  30. ncbi request reprint Transcriptional control of the quorum sensing response in yeast
    Arthur Wuster
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Mol Biosyst 6:134-41. 2010
    ..cerevisiae quorum sensing and may facilitate the engineering of regulatory circuits for applications such as the expression of heterologous proteins via aromatic alcohols...
  31. pmc High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes
    Benjamin Lang
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nucleic Acids Res 35:6330-7. 2007
    ....
  32. doi request reprint Alternative splicing of intrinsically disordered regions and rewiring of protein interactions
    Marija Buljan
    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
    Curr Opin Struct Biol 23:443-50. 2013
    ..In this manner, the alternative splicing of mRNA coding for disordered segments may contribute to the emergence of new traits during evolution, development and disease...
  33. pmc Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes
    Sarath Chandra Janga
    Laboratory of Molecular Biology, Medical Research Council, Hills Road, Cambridge CB2 0QH, United Kingdom
    Proc Natl Acad Sci U S A 105:15761-6. 2008
    ....
  34. ncbi request reprint The HIRAN domain and recruitment of chromatin remodeling and repair activities to damaged DNA
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 5:775-82. 2006
    ....
  35. pmc DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes
    Varodom Charoensawan
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Mol Cell 47:183-92. 2012
    ..Consistent with this, we show that activators induce more nucleosome disruption upon transcriptional activation than repressors...
  36. pmc The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome
    Subhajyoti De
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Genome Res 19:785-94. 2009
    ..We propose that, in addition to other molecular mechanisms, change in genomic neighborhood is an important factor that drives transcriptome evolution...
  37. pmc Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Trends Genet 24:319-23. 2008
    ..Through a detailed analysis of the latter, we predict components of the system responding to protein-aggregation stress...
  38. pmc A complex network framework for unbiased statistical analyses of DNA-DNA contact maps
    Kai Kruse
    Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nucleic Acids Res 41:701-10. 2013
    ..We anticipate that the complex network framework in conjunction with the randomization of DNA-DNA contact networks will become a widely used tool in the study of nuclear architecture...
  39. ncbi request reprint Molecular signatures of G-protein-coupled receptors
    A J Venkatakrishnan
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nature 494:185-94. 2013
    ..A holistic understanding that integrates molecular and systems biology of GPCRs holds promise for new therapeutics and personalized medicine...
  40. ncbi request reprint Evolutionary selection for protein aggregation
    Natalia Sánchez de Groot
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, U K
    Biochem Soc Trans 40:1032-7. 2012
    ..In the present review, we summarize the current knowledge of the advantages associated with aggregation-prone stretches in proteomes and the strategies that cellular systems have developed to control the aggregation process...
  41. pmc Spial: analysis of subtype-specific features in multiple sequence alignments of proteins
    Arthur Wuster
    Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 1TP, UK
    Bioinformatics 26:2906-7. 2010
    ..Spial may also be used to detect residues that may be post-translationally modified in one of the two sets of sequences...
  42. pmc A time-invariant principle of genome evolution
    Subhajyoti De
    Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
    Proc Natl Acad Sci U S A 107:13004-9. 2010
    ..We discuss implications for genome evolution, GWAS, disease genomics, and gene therapy and emphasize the need to investigate both types of mutations within a single framework...
  43. doi request reprint Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica: Non-adaptive forces such as elevated mutation rates may influence the evolution of genome architecture
    Sreenivas Chavali
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK
    Bioessays 33:592-601. 2011
    ..The knowledge of unique genomic features and splicing mechanisms in O. dioica may be exploited for synthetic biology applications, such as generation of orthogonal splicing systems...
  44. ncbi request reprint Investigating transcriptional regulation: from analysis of complex networks to discovery of cis-regulatory elements
    Rekin s Janky
    Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB20QH, United Kingdom
    Methods 48:277-86. 2009
    ..Here we review some of the available computational methodologies for studying transcriptional regulatory networks as well as their interpretation...
  45. pmc Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks
    Marija Buljan
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Mol Cell 46:871-83. 2012
    ..In this way, tissue-specific splicing may contribute to functional versatility of proteins and increases the diversity of interaction networks across tissues...
  46. pmc Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans
    Katherine P Weber
    Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
    PLoS ONE 5:e13922. 2010
    ..Many of these changes modify genome annotation. Our study provides a starting point to further investigate genotype-phenotype association and offers insights into the process of selection as a result of laboratory domestication...
  47. pmc Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks
    Nitish Mittal
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
    Proc Natl Acad Sci U S A 106:20300-5. 2009
    ..Future studies uncovering the posttranscriptional networks in higher eukaryotes can help our understanding of the link between different levels of regulation and their role in pathological conditions...
  48. ncbi request reprint The rules of disorder or why disorder rules
    Jörg Gsponer
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
    Prog Biophys Mol Biol 99:94-103. 2009
    ..In addition, we discuss how such properties, individually and in combination, facilitate combinatorial regulation and re-use of the same component in multiple biological processes...
  49. ncbi request reprint Predicting the strongest domain-domain contact in interacting protein pairs
    Tom M W Nye
    Medical Research Council Biostatistics Unit
    Stat Appl Genet Mol Biol 5:Article5. 2006
    ....
  50. pmc Network-based approaches for linking metabolism with environment
    Sarath Chandra Janga
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Genome Biol 9:239. 2008
    ..Progress in the reconstruction of genome-wide metabolic maps has led to the development of network-based computational approaches for linking an organism with its biochemical habitat...
  51. ncbi request reprint Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells
    Daniel Hebenstreit
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Curr Opin Cell Biol 24:350-8. 2012
    ..These processes and their interplay will also govern gene expression patterns in the different CD4+ cell types, and the determination of their cellular fates...
  52. pmc Interplay between gene expression noise and regulatory network architecture
    Guilhem Chalancon
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
    Trends Genet 28:221-32. 2012
    ..Finally, we highlight recent technological developments that permit measurements at the single-cell level, and discuss directions for future research...
  53. ncbi request reprint Adaptive evolution by optimizing expression levels in different environments
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Microbiol 14:11-4. 2006
    ..These studies clarify how adaptation could occur by the alteration of gene expression...
  54. pmc Conservation and evolutionary dynamics of the agr cell-to-cell communication system across firmicutes
    Arthur Wuster
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
    J Bacteriol 190:743-6. 2008
    ..This suggests that the regulatory network controlled by agr is dynamic and evolves rapidly...
  55. ncbi request reprint Genomic neighbourhood and the regulation of gene expression
    Subhajyoti De
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Curr Opin Cell Biol 22:326-33. 2010
    ..Understanding the role of genomic neighbourhood on gene regulation has fundamental implications for evolution, development, disease and genetic engineering...
  56. pmc Xpf and not the Fanconi anaemia proteins or Rev3 accounts for the extreme resistance to cisplatin in Dictyostelium discoideum
    Xiao Yin Zhang
    Medical Research Council, Laboratory for Molecular Biology, Cambridge, United Kingdom
    PLoS Genet 5:e1000645. 2009
    ..Other DNA damage-resistant organisms and chemoresistant cancer cells might adopt a similar strategy to develop resistance to DNA crosslinking agents...
  57. pmc Evolving nature of the AP2 alpha-appendage hub during clathrin-coated vesicle endocytosis
    Gerrit J K Praefcke
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    EMBO J 23:4371-83. 2004
    ..In the final coated vesicle, most appendage binding partners are absent and thus the functional status of the appendage domain as an interaction hub is temporal and transitory giving directionality to vesicle assembly...
  58. doi request reprint Human inositol polyphosphate multikinase regulates transcript-selective nuclear mRNA export to preserve genome integrity
    Vihandha O Wickramasinghe
    The Medical Research Council Cancer Unit, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
    Mol Cell 51:737-50. 2013
    ..Our findings implicate IPMK in a transcript-selective mRNA export pathway controlled by phosphoinositide turnover that preserves genome integrity in humans. ..
  59. ncbi request reprint Mechanistic insight into site-restricted monoubiquitination of FANCD2 by Ube2t, FANCL, and FANCI
    Arno F Alpi
    Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Mol Cell 32:767-77. 2008
    ..This work therefore establishes a system that provides mechanistic insight into the functions of FANCL and FANCI in the catalysis of FANCD2 monoubiquitination...
  60. pmc Subunit-selective N-terminal domain associations organize the formation of AMPA receptor heteromers
    Maxim Rossmann
    Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
    EMBO J 30:959-71. 2011
    ..Our findings reveal that distinct NTD properties set the stage for the biogenesis of functionally diverse pools of homo- and heteromeric AMPAR tetramers...
  61. ncbi request reprint Shigella apyrase--a novel variant of bacterial acid phosphatases?
    M Madan Babu
    Centre for Biotechnology, Anna University, 600 025, Chennai, India
    FEBS Lett 512:8-12. 2002
    ..It revealed interesting structure-function relationships and probable roles relevant to pathogenesis...
  62. ncbi request reprint Genomic analysis of regulatory network dynamics reveals large topological changes
    Nicholas M Luscombe
    Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, Connecticut 06520 8114, USA
    Nature 431:308-12. 2004
    ..We anticipate that many of the concepts presented here--particularly the large-scale topological changes and hub transience--will apply to other biological networks, including complex sub-systems in higher eukaryotes...
  63. ncbi request reprint GenCompass: a universal system for analysing gene expression for any genome
    Nicholas M Luscombe
    Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520 8114, USA
    Trends Biotechnol 22:552-5. 2004
    ..First, it requires prior knowledge of the DNA sequence encoded in the organism of interest, and second, chips must be designed specifically for each genome, greatly increasing the initial cost incurred in manufacturing the arrays...
  64. ncbi request reprint Registering alpha-helices and beta-strands using backbone C-H...O interactions
    S Kumar Singh
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Proteins 51:167-71. 2003
    ..Modeling studies revealed ready accommodation of serine residues along the helix face that contacts the strand. The theoretically generated folds correspond to "open" polypeptide structures...
  65. ncbi request reprint Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins
    S Chakkaravarthi
    School of Biotechnology and Chemical Engineering, Vellore Institute of Technology, Vellore, India
    Proteins 65:75-86. 2006
    ....
  66. ncbi request reprint Investigations on C-H...pi interactions in RNA binding proteins
    Anand Anbarasu
    School of Bio Technology, Chemical and Bio Medical Engineering, VIT University, Vellore 632014, India
    Int J Biol Macromol 41:251-9. 2007
    ..Seven percent of the theoretically predicted stabilizing residues were also involved in C-Hcdots, three dots, centeredpi interactions and hence these residues may also contribute additional stability to RNA binding proteins...